http://betterlivingthroughchemistry.ghost.io/Ghost 0.11Fri, 16 Mar 2018 16:32:24 GMT60My review of version 7 of potential ChemDraw-slayer ChemDoodle is online at Chemistry World, where it seems to have fallen through some sort of time vortex:

Is ChemDoodle the, erm, future of chemical drawing software?

Obviously you should go and read the whole thing, but spoiler: I like it.

]]>http://betterlivingthroughchemistry.ghost.io/chemdoodle-7-review-for-chemistry-world/65464a63-833f-4443-a56c-32e49b672707Tue, 13 Jan 2015 09:50:44 GMTMy review of version 7 of potential ChemDraw-slayer ChemDoodle is online at Chemistry World, where it seems to have fallen through some sort of time vortex:

Is ChemDoodle the, erm, future of chemical drawing software?

Obviously you should go and read the whole thing, but spoiler: I like it.

]]>Most of us aren't going to win a Nobel Prize this week, or any other week for that matter. I'm gradually coming to accept that I'll probably never top the UK Mathematical Challenge Gold Award & Best in School that I won aged 17&]]>http://betterlivingthroughchemistry.ghost.io/twitter-bombing-the-nobel-announcements/21f7f803-9bc6-4d1e-be00-a1503f4be5a8Tue, 07 Oct 2014 19:15:38 GMTMost of us aren't going to win a Nobel Prize this week, or any other week for that matter. I'm gradually coming to accept that I'll probably never top the UK Mathematical Challenge Gold Award & Best in School that I won aged 17—not as impressive as it sounds (if ever it sounded impressive at all), since my school was, shall we say, less than illustrious. But that doesn't mean there's no fun to be had for those of who won't be waiting by the phone (or, as is apparently the fashion this year, boarding a long-haul flight) tomorrow morning.

So how to entertain ourselves this week? Sylvain Deville suggests prank-calling colleagues:

If you speak English with a Swedish accent, it's the best week of the year to place prank phone calls to your colleagues. #Nobel2014

Anything tweet including #nobelprize2014 appears in the feed, initially unfiltered. It's certainly the closest I'll get to active involvement in a Nobel Prize announcement. It seems that there is someone behind the scenes removing spurious tweets—my effort below disappeared after 10 minutes or so, although I maintain that it was a reasonable enquiry.

Assuming you're quick on the screen-grab, you can then tweet the image alongside the hashtag for multi-level meta goodness.

Now to think of something funnycrudeirreverent respectful to insert into tomorrow's chemistry proceedings.

Fairly typical for organic synthesis types, I would imagine. There are a few big misses in the d-block, and I'm a bit surprised that I never had cause to use any scandium-based Lewis acids, or anything with an SbF6− counterion, but 45 is not a bad haul.

Really impressive would be significant incursions into the f-block or the transactinides.

]]>Something of a dog-bites-man headline, true. That's rarely the case at C&EN Onion, where there's a fair chance of reading about almost anything being bitten by almost anything else, up to and including an emeritus professor.

]]>http://betterlivingthroughchemistry.ghost.io/area-blogger-publishes-improbable-incoherent-story/e31e36a5-e659-4754-a547-0ff13135a2dcTue, 12 Aug 2014 21:03:11 GMTSomething of a dog-bites-man headline, true. That's rarely the case at C&EN Onion, where there's a fair chance of reading about almost anything being bitten by almost anything else, up to and including an emeritus professor.

Birthed from the wild, joyful abandon of #CENOnion and hopping seamlessly from micro- to macroblogging in a manoeuvre that leading tech analysts have already christened “the Internet of Things” (check this—Ed.), this vital news organ provides unparalleled coverage of the chemical sciences.

]]>http://betterlivingthroughchemistry.ghost.io/self-referencing-journal-cover/a545be34-7680-4a1a-b914-7615bff3e6a9Sun, 10 Aug 2014 16:36:25 GMTOne for Chemically Cultured, perhaps. I notice that the cover of the current issue of Green Chemistry has something of a meta aspect to it—it's a cartoon including, amongst other things, an issue of Green Chemistry.

I would have gone the whole hog and drawn1 the same cartoon on the cover of the issue within the cartoon, despite the risk of tumbling into an abyss of infinite recursion.

1. Very much hypothetical. Chemical structures aside, I can't draw for toffee. ↩

]]>

Or love me less, or love me moreAnd play not with my libertyEither take all, or all restoreBind me at least, or set me free
—Sidney Godolphin

I've recently noticed some journals where all the content is free on one website, but a publisher is charging for access to the same stuff on another. Two examples: the legendary Organic Syntheses and, slightly off my personal beaten track, the Journal of Allergy and Clinical Immunology. Visit the Org. Synth. website, say because you want to whip up some CBS catalyst, and no matter whether you're accessing via diamond-encrusted WiFi from the tallest ivory tower of your storied academic institution, which subscribes to everything up to and including Heterocycles, or squinting through the gloom in a grubby internet café in Ulan Bator, you can see the paper. Try to access the same article on Wiley's site, on the other hand—no dice, unless you're a subscriber.

At this time of year hay-fever sufferers might well want to read up on fluticasone furoate, and J. Allergy Clin. Immunol. is as good a place as any. Once again, on the journal's own site, the paper is free, but over on ScienceDirect, Elsevier will try to skin you for $36. Note that we're not talking author manuscripts here; the free article is the typeset, final article of scientific record.1 Nor are we dealing with articles uploaded here and there, (technically) in breach of copyright. These are official sites hosting the entirety of the journals' content, with, I can only assume, the full knowledge and consent of the respective publishers.

Now, an obvious response would be that since both are there on the internet for people to see, the market will vote with its feet. The problem with that, though, is one of discoverability. You can only take advantage of the free version if you can find it. Neither of these examples are particularly hard to find… if you know to look for them. Very often, people will arrive at a paper via a DOI—if you come from SciFinder, Reaxys, Web of Science, PubMed or anything like that, you'll be directed to the paper through a DOI resolver. And guess what? The Wiley Org. Synth. articles have different DOIs to the free ones. The literature databases that I tried did contain the DOI pointing at the free Org. Synth. site, which is something, but I've no doubt that the Wiley DOIs are out there, lying in wait for the unsuspecting reader.

The J. Allergy Clin. Immunol. example is odder still. I could only find one DOI per article (10.1016/j.jaci.2007.02.022 for the article linked above), but it can lead you to either site. However you end up following that DOI (SciFinder etc., or directly from dx.doi.org), it sends you first to ‘linkinghub.elsevier.com’, which seems to make a decision where to redirect you based on what type of user you appear to be. At home (not quite the Ulan Bator internet café, but with a similar level of journal access), I was redirected to the site with the free articles. Hurrah! But at work, the same DOI sent me to ScienceDirect and their paywall. I assume this is because ScienceDirect saw me as a ‘customer’—we have IP-authenticated access to a handful of Elsevier journals, none of them J. Allergy Clin. Immunol.—but why that means we can just be ushered away from the free content is baffling. Two questions spring to mind: what would CrossRef make of the same DOI taking you to two different places, and more importantly, why does the ScienceDirect journal page exist at all? Selling something that you know to be freely available elsewhere is fundamentally dishonest.

I don't know how widespread this kind of set-up is, and I don't know why these journals have this weird arrangement. Org. Synth. is admittedly a bit of an oddity in other ways, but J. Allergy Clin. Immunol. is, as far as I can see, a fairly standard sort of journal. Whatever the reason for it, it seems that once again in scientific publishing, the customers—researchers, librarians, funders—are getting the short end of the stick.

1. The value of an edited article vs the authors' original is another question for another day. ↩

Connoisseurs can find the same text in all its typeset glory here ($, but ReadCube's first-page preview is particularly generous when an article only

]]>http://betterlivingthroughchemistry.ghost.io/on-a-roll/d5c306ca-3592-4ea9-8e2f-7b36cb961013Fri, 20 Jun 2014 20:24:26 GMTAlthough I've not posted here in a while (soon, honest), I did the honours for this month's Nature Chemistry Blogroll column.

Connoisseurs can find the same text in all its typeset glory here ($, but ReadCube's first-page preview is particularly generous when an article only occupies a third of a page).

]]>There's nothing wrong with a forward-looking, what-might-the-future-hold journal article. Something that looks beyond the current state-of-the-art and discusses which advances might soon revolutionise a field of science.

Nothing wrong with that at all.

Unless, of course, said article is about as grounded in reality as David Icke on

]]>http://betterlivingthroughchemistry.ghost.io/drugprinter-or-the-hallucinogenic-goose-that-3d-prints-the-golden-egg/66698f95-b6ff-4040-9942-7370062a2842Sat, 19 Apr 2014 16:32:44 GMTThere's nothing wrong with a forward-looking, what-might-the-future-hold journal article. Something that looks beyond the current state-of-the-art and discusses which advances might soon revolutionise a field of science.

Nothing wrong with that at all.

Unless, of course, said article is about as grounded in reality as David Icke on homeopathic crack.

Twitterers of a chemical bent will probably already have seen the offending article, but for the benefit of the rest of you, it's here. It's open access—science of such vision shall be constrained by no paywall.

I'm tempted to go through this line-by-line, but I'm moving house this weekend, so I'll spare you. The gist is that the author has been granted a rare glimpse into the future of drug manufacture, and it involves his DrugPrinter (a prototype from his lab is predicted within five years, and the fully realised technology within 20). The DrugPrinter would manoeuvre each atom (yes, each ATOM) into position by a means as yet unknown (see fig. 5 for some options), thus rendering all current synthetic efforts obselete.

You really need to read the whole paper to get a full measure of the crazy, but as a teaser, here's a putative benzene synthesis:

(I'd credit Elsevier for the image, but I imagine that once they get into the office next week they'll be sprawling sideways to avoid any of the ‘credit’ for this abomination.)

Update Apr 23rd, 2014: It seems that the author has responded, mainly in the comments of Quintus's blog. The somewhat surreal exchange includes what are apparently some of the referee comments and the author's responses to them.

A few things that stand out:

According to the author, the review process involved no fewer than three referees and two editors, and a number of rounds of revision. It's a little difficult to get a handle on the views of the referees, as the comments appear to be incomplete, but they appear to have raised at least some of the same issues as various bloggers and commenters. The real problem seems to be the reviewers' (or editors', or both) acceptance of the author's responses, which mostly (at least from what has been posted) fail to address the glaring problems. It's baffling that five pairs of eyes have looked at this and, although they obviously had some reservations, none of them have seen the wood beyond the trees, namely the article's total lack of suitability for publication in a scholarly journal.

If the commenter is indeed the author, then he seems genuine in his concocting and submitting the article, and somewhat distraught at the criticism it's received. While the scientific aspects of the criticism are entirely justifed, perhaps it has strayed too much into the personal at times (and I include myself in that). The author says he has asked the editor of Drug Discovery Today to withdraw the article, and the editor has agreed, so maybe it's now best to let this lie.

More of a concern than this bizarre article, I would say, is the failure of the peer review system that allowed it to be published in the first place. It would be nice to hear something from Drug Discovery Today, although I expect little more than a vague notice saying ‘retracted at the author's request’.

Update Apr 28th, 2014: The article has now been withdrawn.

All that remains is the following note from the publisher:

This article has been withdrawn at the request of the author. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.

Given that the publication of these articles is evidence of a systematic problem with editorial processes, we have placed Springer's membership of OASPA ‘under review’, pending a thorough response and description of the steps that are being taken to strengthen the necessary processes.

…ACS Publications, like other information providers, utilizes a number of standard protocols that strike a balance between ease of accessibility for the scientific community and the necessary protection of technical infrastructure.

Early on Thursday, April 3, a link was posted to Twitter that exposed one such tool—a “spider trap” designed to prevent unlicensed machine-aided crawling and data extraction activity—that resulted in the temporary disablement of access for a number of ACS' institutional customer accounts.

ACS worked diligently to resolve the issue, and as of 4 PM EDT April 3, service was restored for all subscribers affected by this incident. Simultaneously, steps were taken to address the specific protocol that triggered this outage.

We regret the lapse in service, and we would like to assure you that ACS Publications will continue to serve the broader audience of chemical professionals, including customers, members and the scientific community who value access to the high quality, trusted original research published in ACS journals. Employing the use of these types of tools is imperative to providing users with continued access to that trusted research. We will therefore continue to refine our security procedures to support evolving publishing access models while protecting both users and content from malicious activities.

Secondly, as PMR details, the story reached Hacker News, where the ensuing discussion illuminated some of Thursday's mysteries. It seems that pubs.acs.org sits on a platfrom provided by a third party, Atypon, whose clients include Elsevier, IEEE, Informa Healthcare/Taylor & Francis, OUP and Thieme. This explains the spider trap appearing in exactly the same form across a number of publishers' sites, and the DOI-esque link's odd combination of a Wiley prefix and an Informa landing page.

The really eye-catching development, though, relates to a comment posted on PMR's second blog post on the subject. Context: when initially relating Pandora's experience, Peter recalled that the University of Cambridge had been cut off by the ACS in a similar fashion several years earlier, when one of his students had inadvertently triggered a rapid-reading monitor by (humanly) downloading 20-odd papers in quick succession. Peter had mentioned this (and the reason for it, i.e., not a spider trap) twice when a commenter, Georgios Papadopoulos, sailed in with this, quoting Peter in the first line:

> Note that my own experience was not a spider trap but simply (humanly) reading too many papers too rapidly – publications are not meant to be read rapidly, are they?

This is really funny. Tom Demeranville described the trap very acurately.

These LINKS (they are not DOIs!) are not visble or clickable. Only a (dumb) spider follows them. You created such a dumb spider and you were scraping the content. You were not reading it or clicking on anything.

You were caught, but perhaps the funniest part of that was that then you also came up and exposed yourself. We usually never identify the writers of such crawlers.

At first glance, an ill-informed troll. However, once the involvement of Atypon was revealed, the name Georgios Papadopoulos suddenly gained significance—he's Atypon's CEO.

Of course, it could be an imposter, but Peter doesn't believe so. If that really comes from the Atypon CEO, it's quite staggering in its ignorance and arrogance. Someone stumbles across a ‘security measure’ deployed by your company, a measure of irresponsibly poor execution, and the internet investigates. Your response? Wade in to the comments on a blog and gloat about it, simaltaneously displaying either an unwillingness or an inability to read and understand some fairly simple circumstances described on that blog. Wow.

No doubt there's more to come—what the ACS will do about it being of primary interest.

]]>Hijinks and outrage on Twitter today, after the discovery of a spider trap embedded in the pages of the ACS journal platform.

It first came to light via Peter Murray-Rust's blog, where he reported that the enigmatic ‘Pandora’ had found herself and her institution blocked from

]]>http://betterlivingthroughchemistry.ghost.io/the-acs-in-spiderland/1e887190-53e1-44c5-bae7-bffe16a930d1Thu, 03 Apr 2014 17:57:26 GMTHijinks and outrage on Twitter today, after the discovery of a spider trap embedded in the pages of the ACS journal platform.

It first came to light via Peter Murray-Rust's blog, where he reported that the enigmatic ‘Pandora’ had found herself and her institution blocked from pubs.acs.org in its entirety, after first uncovering and then, understandably curious, clicking on the poisoned link.

The result? This message:

This link in question looks like an article DOI, presumably so that a web crawler attempting to aggregate ACS articles would gobble it up, before finding itself unceremoniously banned.

It's not visible on the journal pages themselves; rather it's hidden in the underlying HTML. However, once found, a simple web link can get anywhere.

Judging by the Twitter reaction, a number of people followed the link from the blog post, either not realising the consequences, or seeing it as online activism to highlight the ACS's behaviour. Cue blocked institutions, with Nature Publishing Group among the victims.

Things kicked off further after Ross Mounce, perhaps somewhat ill-advisedly, included the link in a tweet without much context. Angryreactions followed, as more people clicking the dread link found themselves unwitting activists, and found their institution's IP range out in the cold. That said, a large part of that anger was (rightly in my opinion) directed towards the ACS.

Alarmingly/amusingly, depending on your point of view, it was briefly feared that the entire Portuguese university system had lost access, due to its consortium subscription. Apparently not.

Also emerging was a degree of confusion as to what the link was and how it got there. I'm not going to post the link itself (don't want any more casualties), but here's what it looks like:

Although not, as pointed out by CrossRef, a true DOI, it's in the standard format of the ACS platform, e.g., http://pubs.acs.org/doi/abs/10.1021/es405402r (the level after ‘doi’ is ‘abs’ or ‘pdf’ or ‘full’ depending on whether it points to the abstract page, pdf, or HTML full text). What's odd, though, is that it has the DOI prefix 10.1046. As can be seen in the standard ACS url above, their prefix is 10.1021. 10.1046 belongs to Blackwell, now part of Wiley. And the landing page that the DOI points to apparently belongs to yet another publisher, Informa.

On Twitter, CrossRef surmised that this meant it was a prank. However, since link-clickers were not simply seeing a warning message, but were finding themselves comprehensively banned from pubs.acs.org, that seems unlikely. While these things are hardly my specialist subject, it seems that it would be difficult enough for an outside agent just to slip this link into HTML of the ACS platform, nevermind imposing a block on those who followed it.

Presumably after receiving record levels of correspondence to ipblock@acs.org, the ACS issued a response of sorts, in the comments of PMR's blog:

Thank you for alerting us to the finding shared by your reader. We are exploring and are committed to providing text and data mining solutions for readers of our open access content. In the meantime, for those who have unfortunately clicked on the link referenced and received the spider message, please email support@services.acs.org with your institution name and we will work to reinstate access at your institution as quickly as possible.Darla Henderson, Ph.D.Asst. Director, Open Access ProgramsAmerican Chemical Society

This touches on another issue: aside from the clumsy and irresponsible way that the ACS have blocked any attempt at data mining, the paper that originally triggered the avalanche was open access. Why are the ACS blocking data mining of a paper when the authors (or their funders) have paid to make it freely available?2

All in all, it seems like a massive internet fail on the part of the ACS. Despite lacking any particular expertise in such things, the failings of their spider trap are not difficult to see. I'm told that there are better and more responsible ways to achieve this (where appropriate! Don't try to lock up open access content), and I trust that the ACS are currently thinking hard about some of them.

Ok, we all know SciFinder lies sometimes. It's not always their fault, sometimes the reaction they've faithfully indexed and you've faithfully, hopefully, please-Lord-let-this-one-work-ully set up never really gave the yield the authors said it did in the first place.

Ok, we all know SciFinder lies sometimes. It's not always their fault, sometimes the reaction they've faithfully indexed and you've faithfully, hopefully, please-Lord-let-this-one-work-ully set up never really gave the yield the authors said it did in the first place.

But this is just taking the piss.

Look at the responses on Twitter and in the comments of the Synthetic Remarks blog linked above. Their repeated refusal to admit that the example quoted is total nonsense, indeed their apparent refusal even to cast an eye over it, speaks very poorly of their commitment to accuracy and to correcting errors, which I would expect to be at the heart of their business.

The CAS registry and SciFinder contain a huge amount of important data. Please reassure us that you value its accuracy.

]]>Richard Van Noorden in Nature reports that 120-odd published conference proceedings are to be withdrawn, after it was pointed out that they were products of ingenious drivel-generator SCIgen.

Well, the hook this time is that the egg is on the faces of publishers you've actually

]]>http://betterlivingthroughchemistry.ghost.io/credulous-publishers-accept-nonsensical-papers/a978c051-f96f-440e-8695-76bdb37ff590Tue, 25 Feb 2014 23:29:00 GMTRichard Van Noorden in Nature reports that 120-odd published conference proceedings are to be withdrawn, after it was pointed out that they were products of ingenious drivel-generator SCIgen.

Well, the hook this time is that the egg is on the faces of publishers you've actually heard of, namely Springer and IEEE, rather than the predatory types found at the villainous end of the Open Access world.

Director of corporate communications Monika Stickel is quoted as saying that IEEE have:

refined our processes to prevent papers not meeting our standards from being published in the future

Refinements that presumably include reading submitted papers.

Interestingly, Springer's Ruth Francis apparently confirmed to Nature that the offending papers were peer-reviewed. When a predatory OA journal gets stung like this, their motive for publishing anything and everything is clear—author fees. I've always assumed that those publishers don't bother with peer review at all, or that a fraction of papers are reviewed to give some veneer of respectability. However, it's difficult to see what subscription-based publishers like IEEE and Springer would gain from uncritically accepting garbage, and, assuming that these articles were reviewed, I find it hard to believe that so many referees could be so incompetent.

Working for a scientific publisher of some repute, I've seen many referee reports that leave a distinct impression of ‘nodding a paper through’ without a proper evaluation, but never the lack-of-giving-a-fuck that would be required to give a SCIgen paper the green light. Even if, like me, you're almost entirely unversed in computer science research, reading the SCIgen articles reveals them as incoherent nonsense pretty quickly. It's surely unthinkable that an expert referee would be fooled.

So what's going on? Are Springer lying when they say the papers were peer-reviewed? If so, why would they gamble their credibility for no apparent benefit? Or are there referees who, confronted with work supposedly in their field that they couldn't make head-nor-tail of, didn't have the confidence to call it out, and instead assumed they were missing something and gave a vague approval? Could that be compounded by a less-than-perfect grasp of English? I struggle to imagine being confronted with the (generally) grammatically correct yet logically challenged SCIgen text as a non-native English speaker.

If a chemistry SCIgen-equivalent existed, I'd bet the farm on its faux-papers being laughed out by the referees that I've worked with, if they ever got that far.

That said, I'm now tempted to test that theory.

Update Feb 27th, 2014: Another Nature News article covering the publishers' responses. Springer are removing the fake articles, but leaving a note on the page explaining what used to be there.

IEEE, on the other hand, are apparently just purging them, leaving nothing but a 404 behind. Not cool.

]]>Bit late on this… to celebrate Darwin Day, here's Baba Brinkman's hip-hop tribute to Darwin and to biology teachers who refuse to dilute the scientific content of origins-of-life discussions:

I came across the video on Larry Moran's blog, where he expresses concern over the glorification of Darwin. Larry's problem

I came across the video on Larry Moran's blog, where he expresses concern over the glorification of Darwin. Larry's problem is that it implies that Darwinism accounts for all evolutionary theory, and that it shares some aspects with a religious movement.

My view is that you can celebrate a giant of science without creating a cult. I think the the simplification is justified – any time you try to make something complex accessible to the general public, simplification is inevitable. Those who are interested enough to investigate further will quickly find out that there's more to it than just Darwin.

And as a fan of ill-advised, earnest rap, I really like the track.

]]>I've started one of these ‘web-logs’ that have proved unfathomably popular with today's youth.

I don't have all that much to say, but that doesn't seem to have stopped anyone else.

Real content to follow… in the meantime, here's a cracking journal cover:

]]>http://betterlivingthroughchemistry.ghost.io/hello-world/0e5ffa07-c26a-4c67-a29e-5b95fdd1a3d5Sat, 22 Feb 2014 15:31:50 GMTI've started one of these ‘web-logs’ that have proved unfathomably popular with today's youth.

I don't have all that much to say, but that doesn't seem to have stopped anyone else.

Real content to follow… in the meantime, here's a cracking journal cover: